how to use a chromosome scale reference genome to place scaffold of a closely related species

Question

[nagarsaggi]

We have recently sequenced a close wild relative of pigeonpea using PacBio and scaffold the contigs with optical mapping. Now I would like to place/assign those scaffold to the chromosome. Hence, I was wondering how to use the reference genome of pigeonpea which is a chromosome scale for placing scaffold of its wild relative to chromosomes. Please suggest any tool or strategy.

Answer 1

[Michael]

Mauve should work for that. Has a GUI viewer for inspecting alignments too and handles more than two species if required.

The web-site says it is no longer maintained but as long as it works for you it should be fine. Can be installed with BioConda.